3V85 | pdb_00003v85

1.9 Angstrom resolution crystal structure of the protein Q9SIY3 from Arabidopsis thaliana

PDB DOI: https://doi.org/10.2210/pdb3V85/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-12-22 Released: 2012-11-07
Deposition Author(s): Garcia, C., Fucile, G., Petit, P., Christendat, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A yeast-like mRNA triphosphatase from Arabidopsis thaliana

Garcia, C., Fucile, G., Moeder, W., Christendat, D., Yoshioka, K.

To be published.

Macromolecule Content

Total Structure Weight: 24.39 kDa
Atom Count: 1,811
Modelled Residue Count: 204
Deposited Residue Count: 210
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTH-like phosphatase	A	210	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At2g11890 EC: 3.6.1 (UniProt), 3.6.1.25 (UniProt)
UniProt
Find proteins for Q9SIY3 (Arabidopsis thaliana) Explore Q9SIY3 Go to UniProtKB: Q9SIY3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9SIY3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.776	α = 90
b = 33.952	β = 95.23
c = 71.596	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Christendat, D.

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.